git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-34 - quick hack to see how we can do alignment comparison for splitframes linking...
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeModel.java
diff --git
a/src/jalview/analysis/TreeModel.java
b/src/jalview/analysis/TreeModel.java
index
90fe089
..
1068042
100644
(file)
--- a/
src/jalview/analysis/TreeModel.java
+++ b/
src/jalview/analysis/TreeModel.java
@@
-353,7
+353,9
@@
public class TreeModel
if ((nd.left() == null) && (nd.right() == null))
{
if ((nd.left() == null) && (nd.right() == null))
{
- jalview.bin.Console.outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
+ // TODO FIX FOR COLUMN TREES
+ jalview.bin.Console
+ .outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
jalview.bin.Console.outPrintln("Dist " + nd.dist);
jalview.bin.Console.outPrintln("Boot " + nd.getBootstrap());
}
jalview.bin.Console.outPrintln("Dist " + nd.dist);
jalview.bin.Console.outPrintln("Boot " + nd.getBootstrap());
}
@@
-430,7
+432,7
@@
public class TreeModel
if ((nd.left() == null) && (nd.right() == null))
{
if ((nd.left() == null) && (nd.right() == null))
{
- nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
+ nd.height = nd.parent().height + nd.dist;
if (nd.height > maxheight)
{
if (nd.height > maxheight)
{
@@
-445,7
+447,7
@@
public class TreeModel
{
if (nd.parent() != null)
{
{
if (nd.parent() != null)
{
- nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
+ nd.height = nd.parent().height + nd.dist;
}
else
{
}
else
{
@@
-480,7
+482,8
@@
public class TreeModel
}
else
{
}
else
{
- jalview.bin.Console.outPrintln(" name = " + ((SequenceI) nd.element()).getName());
+ jalview.bin.Console.outPrintln(
+ " name = " + ((SequenceI) nd.element()).getName());
}
jalview.bin.Console.outPrintln(
}
jalview.bin.Console.outPrintln(
@@
-513,7
+516,8
@@
public class TreeModel
{
// if (_lycount<_lylimit)
// {
{
// if (_lycount<_lylimit)
// {
- // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than number of
+ // jalview.bin.Console.errPrintln("Warning: depth of _recount greater than
+ // number of
// nodes.");
// }
if (nd == null)
// nodes.");
// }
if (nd == null)